Molecular evolution [electronic resource] : computer analysis of protein and nucleic acid sequences / edited by Russell F. Doolittle.

Includes indexes.

Includes bibliographical references.

GenBank: Current status and future directions / Christian Burks [and others] -- EMBL Data Library / Patricia Kahn and Graham Cameron -- Protein Sequence Database / Winona C. Barker, David G. George and Lois T. Hunt -- Cooperation between databases and scientific community / Borivoj Keil -- Rapid and sensitive sequence comparison with FASTP and FASTA / William R. Pearson -- Searching through sequence databases / Russell F. Doolittle -- Finding protein similarities with nucleotide sequence databases / Steven Henikoff, James C. Wallace and Joseph P. Brown -- Use of homology domains in sequence similarity detection / Charles B. Lawrence -- Profile analysis / Michael Gribskov, Roland Lothy and David Eisenberg -- Finding protein coding regions in genomic sequences / Rodger Staden -- Ancient patterns in nucleic acid sequences / John C.W. Shepherd -- Searching for patterns in protein and nucleic acid sequences / Rodger Staden -- Consensus patterns in DNA / Gary D. Stormo -- Consensus methods for DNA and protein sequence alignment / Michael S. Waterman and Robert Jones -- k-tuple frequency analysis: From intron/exon discrimination to T-cell epitope mapping / Jean-Michel Claverie, Isabelle Sauvaget and Lydie Bougueleret -- Splice junctions, branch point sites, and exons: Sequence statistics, identification, and applications to genome project / Periannan Senapathy, Marvin B. Shapiro and Nomi L. Harris -- Predicting optimal and suboptimal secondary structure for RNA / John A. Jaeger, Douglas H. Turner and Michael Zuker -- Detecting pseudoknots and other local base-pairing structures in RNA sequences / Hugo M. Martinez -- Computer modeling and display of RNA secondary and tertiary structures / Daniel Gautheret, Fran�cois Major and Robert Cedergren.

Mutation data matrix and its uses / David G. George, Winona C. Barker and Lois T. Hunt -- Sensitivity comparison of protein amino acid sequences / Patrick Argos and Martin Vingron -- Three-way Needleman--Wunsch algorithm / Mitsuo Murata -- Progressive alignment and phylogenetic tree construction of protein sequences / Da-Fei Feng and Russell F. Doolittle -- Identification of significant sequence patterns in proteins / Samuel Karlin, B. Edwin Blaisdell and Volker Brendel -- Protein multiple sequence alignment and flexible pattern matching / Geoffrey J. Barton -- Genomic divergence through gene rearrangement / David Sankoff, Robert Cedergren and Yvon Abel -- Multiple sequence comparison / David J. Bacon and Wayne F. Anderson -- Simultaneous comparison of several sequences / Mauno Vihinen -- Hierarchical method to align large numbers of biological sequences / William R. Taylor -- Significance of protein sequence similarities / John F. Collins and Andrew F.W. Coulson -- Fast alignment of DNA and protein sequences / Gad M. Landau, Uzi Vishkin and Ruth Nussinov -- Statistical geometry on sequence space / Manfred Eigen and Ruthild Winkler-Oswatitsch -- Statistical methods for estimating sequence divergence / Takashi Gojobori, Etsuko N. Moriyama and Motoo Kimura -- Converting distance to time: Application to human evolution / Hirohisa Kishino and Masami Hasegawa-- Influence of base composition on quantitative estimates of gene evolution / Cecilia Saccone [and others] -- Maximum likelihood methods / Naruya Saitou -- Maximum parsimony approach to construction of evolutionary trees from aligned homologous sequences / John Czelusniak [and others] -- Phylogeny determination using dynamically weighted parsimony method / Patrick L. Williams and Walter M. Fitch-- Unified approach to alignment and phylogenies / Jotun Hein -- Statistical tests of molecular phylogenies / Wen-Hsiung Li and Manolo Gouy -- Nearest neighbor procedure for relating progressively aligned amino acid sequences / Russell F. Doolittle and Da-Fei Feng -- Phylogenetic relationships from three-dimensional protein structures / Mark S. Johnson, Andrej Sali and Tom L. Blundell.

This volume addresses a variety of areas in which computers are used to manage and manipulate nucleic acid and protein sequence data. The manipulations include searching, aligning, and determining the significance of similarities, as well as the construction of phylogenetic trees that show the evolutionary history of related sequences. Ready-to-use methods for the "at-the-bench" scientist are presented.

Description based on print version record.